PeerJ: (Highly rated) Environmental Science Sectionhttps://peerj.com/articles/index.atom?journal=peerj&section=environ-sci&rating=5 (Highly rated) PeerJ articles published in the Environmental Science SectionA de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technologyhttps://peerj.com/articles/91142020-06-052020-06-05Jiawei WangWeizhen LiuDongzi ZhuXiang ZhouPo HongHongjun ZhaoYue TanXin ChenXiaojuan ZongLi XuLisi ZhangHairong WeiQingzhong Liu
The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.

The sweet cherry (Prunus avium) is one of the most economically important fruit species in the world. However, there is a limited amount of genetic information available for this species, which hinders breeding efforts at a molecular level. We were able to describe a high-quality reference genome assembly and annotation of the diploid sweet cherry (2n = 2x = 16) cv. Tieton using linked-read sequencing technology. We generated over 750 million clean reads, representing 112.63 GB of raw sequencing data. The Supernova assembler produced a more highly-ordered and continuous genome sequence than the current P. avium draft genome, with a contig N50 of 63.65 KB and a scaffold N50 of 2.48 MB. The final scaffold assembly was 280.33 MB in length, representing 82.12% of the estimated Tieton genome. Eight chromosome-scale pseudomolecules were constructed, completing a 214 MB sequence of the final scaffold assembly. De novo, homology-based, and RNA-seq methods were used together to predict 30,975 protein-coding loci. 98.39% of core eukaryotic genes and 97.43% of single copy orthologues were identified in the embryo plant, indicating the completeness of the assembly. Linked-read sequencing technology was effective in constructing a high-quality reference genome of the sweet cherry, which will benefit the molecular breeding and cultivar identification in this species.

Reconstruction of past distribution for the Mongolian toad, Strauchbufo raddei (Anura: Bufonidae) using environmental modelinghttps://peerj.com/articles/92162020-06-052020-06-05Spartak N. LitvinchukNatalya A. SchepinaAmaël Borzée
The use of ecological models enables determining the current distribution of species, but also their past distribution when matching climatic conditions are available. In specific cases, they can also be used to determine the likelihood of fossils to belong to the same species—under the hypothesis that all individuals of a species have the same ecological requirements. Here, using environmental modeling, we reconstructed the distribution of the Mongolian toad, Strauchbufo raddei, since the Last Glacial Maximum and thus covering the time period between the Late Pleistocene and the Holocene. We found the range of the species to have shifted over time, with the LGM population clustered around the current southern range of the species, before expanding east and north during the Pleistocene, and reaching the current range since the mid-Holocene. Finally, we determined that the ecological conditions during the life-time of the mid-Pleistocene fossils attributed to the species in Europe were too different from the one of the extant species or fossils occurring at the same period in Asia to belong to the same species.

The use of ecological models enables determining the current distribution of species, but also their past distribution when matching climatic conditions are available. In specific cases, they can also be used to determine the likelihood of fossils to belong to the same species—under the hypothesis that all individuals of a species have the same ecological requirements. Here, using environmental modeling, we reconstructed the distribution of the Mongolian toad, Strauchbufo raddei, since the Last Glacial Maximum and thus covering the time period between the Late Pleistocene and the Holocene. We found the range of the species to have shifted over time, with the LGM population clustered around the current southern range of the species, before expanding east and north during the Pleistocene, and reaching the current range since the mid-Holocene. Finally, we determined that the ecological conditions during the life-time of the mid-Pleistocene fossils attributed to the species in Europe were too different from the one of the extant species or fossils occurring at the same period in Asia to belong to the same species.

Immune priming against bacteria in spiders and scorpions?https://peerj.com/articles/92852020-06-052020-06-05Dumas GálvezYostin AñinoCarlos VegaEleodoro Bonilla
Empirical evidence of immune priming in arthropods keeps growing, both at the within- and trans-generational level. The evidence comes mostly from work on insects and it remains unclear for some other arthropods whether exposure to a non-lethal dose of a pathogen provides protection during a second exposure with a lethal dose. A poorly investigated group are arachnids, with regard to the benefits of immune priming measured as improved survival. Here, we investigated immune priming in two arachnids: the wolf spider Lycosa cerrofloresiana and the scorpion Centruroides granosus. We injected a third of the individuals with lipopolysaccharides of Escherichia coli (LPS, an immune elicitor), another third were injected with the control solution (PBS) and the other third were kept naive. Four days after the first inoculations, we challenged half of the individuals of each group with an injection of a high dose of E. coli and the other half was treated with the control solution. For scorpions, individuals that were initially injected with PBS or LPS did not differ in their survival rates against the bacterial challenge. Individuals injected with LPS showed higher survival than that of naive individuals as evidence of immune priming. Individuals injected with PBS tended to show higher survival rates than naive individuals, but the difference was not significant—perhaps suggesting a general immune upregulation caused by the wounding done by the needle. For spiders, we did not observe evidence of priming, the bacterial challenge reduced the survival of naive, PBS and LPS individuals at similar rates. Moreover; for scorpions, we performed antibacterial assays of hemolymph samples from the three priming treatments (LPS, PBS and naive) and found that the three treatments reduced bacterial growth but without differences among treatments. As non-model organisms, with some unique differences in their immunological mechanisms as compared to the most studied arthropods (insects), arachnids provide an unexplored field to elucidate the evolution of immune systems.

Empirical evidence of immune priming in arthropods keeps growing, both at the within- and trans-generational level. The evidence comes mostly from work on insects and it remains unclear for some other arthropods whether exposure to a non-lethal dose of a pathogen provides protection during a second exposure with a lethal dose. A poorly investigated group are arachnids, with regard to the benefits of immune priming measured as improved survival. Here, we investigated immune priming in two arachnids: the wolf spider Lycosa cerrofloresiana and the scorpion Centruroides granosus. We injected a third of the individuals with lipopolysaccharides of Escherichia coli (LPS, an immune elicitor), another third were injected with the control solution (PBS) and the other third were kept naive. Four days after the first inoculations, we challenged half of the individuals of each group with an injection of a high dose of E. coli and the other half was treated with the control solution. For scorpions, individuals that were initially injected with PBS or LPS did not differ in their survival rates against the bacterial challenge. Individuals injected with LPS showed higher survival than that of naive individuals as evidence of immune priming. Individuals injected with PBS tended to show higher survival rates than naive individuals, but the difference was not significant—perhaps suggesting a general immune upregulation caused by the wounding done by the needle. For spiders, we did not observe evidence of priming, the bacterial challenge reduced the survival of naive, PBS and LPS individuals at similar rates. Moreover; for scorpions, we performed antibacterial assays of hemolymph samples from the three priming treatments (LPS, PBS and naive) and found that the three treatments reduced bacterial growth but without differences among treatments. As non-model organisms, with some unique differences in their immunological mechanisms as compared to the most studied arthropods (insects), arachnids provide an unexplored field to elucidate the evolution of immune systems.

Genome-wide sequence identification and expression analysis of ARF family in sugar beet (Beta vulgaris L.) under salinity stresseshttps://peerj.com/articles/91312020-06-042020-06-04Jie CuiXinyan LiJunliang LiCongyu WangDayou ChengCuihong Dai
Auxin response factor (ARF) proteins respond to biological and abiotic stresses and play important roles in regulating plant growth and development. In this study, based on the genome-wide database of sugar beet, 16 BvARF proteins were identified. A detailed investigation into the BvARF family is performed, including analysis of the conserved domains, chromosomal locations, phylogeny, exon-intron structure, conserved motifs, subcellular localization, gene ontology (GO) annotations and expression profiles of BvARF under salt-tolerant condition. The majority of BvARF proteins contain B3 domain, AUX_RESP domain and AUX/IAA domain and a few lacked of AUX/IAA domain. Phylogenetic analysis suggests that the 16 BvARF proteins are clustered into six groups. Expression profile analysis shows that most of these BvARF genes in sugar beet under salinity stress were up-regulated or down-regulated to varying degrees and nine of the BvARF genes changed significantly. They were thought to have a significant response to salinity stress. The current study provides basic information for the BvARF genes and will pave the way for further studies on the roles of BvARF genes in regulating sugar beet’s growth, development and responses to salinity stress.

Auxin response factor (ARF) proteins respond to biological and abiotic stresses and play important roles in regulating plant growth and development. In this study, based on the genome-wide database of sugar beet, 16 BvARF proteins were identified. A detailed investigation into the BvARF family is performed, including analysis of the conserved domains, chromosomal locations, phylogeny, exon-intron structure, conserved motifs, subcellular localization, gene ontology (GO) annotations and expression profiles of BvARF under salt-tolerant condition. The majority of BvARF proteins contain B3 domain, AUX_RESP domain and AUX/IAA domain and a few lacked of AUX/IAA domain. Phylogenetic analysis suggests that the 16 BvARF proteins are clustered into six groups. Expression profile analysis shows that most of these BvARF genes in sugar beet under salinity stress were up-regulated or down-regulated to varying degrees and nine of the BvARF genes changed significantly. They were thought to have a significant response to salinity stress. The current study provides basic information for the BvARF genes and will pave the way for further studies on the roles of BvARF genes in regulating sugar beet’s growth, development and responses to salinity stress.

Bee diversity in secondary forests and coffee plantations in a transition between foothills and highlands in the Guatemalan Pacific Coasthttps://peerj.com/articles/92572020-06-042020-06-04Gabriela Armas-QuiñonezRicardo Ayala-BarajasCarlos Avendaño-MendozaRoberto Lindig-CisnerosEk del-Val
Background
Although conservation of pristine habitats is recognized in many countries as crucial for maintaining pollinator diversity, the contribution of secondary forest conservation is poorly recognized in the Latin American context, such as in Guatemala. San Lucas Tolimán (SLT) is a high-quality coffee production region from the Atitlan Province, which has the second highest deciduous forest cover in Guatemala and pristine forest is prioritized for conservation. In contrast, secondary forest protection is undetermined, since these forests are normally removed or strongly affected by coffee farming practices. This situation may affect the diversity of native pollinators, mainly bees, which usually rely on the secondary forest for food resources.
Methods
We conducted a study to investigate the importance of secondary forests around the SLT coffee plantations (Coffea arabica L.) for pollinators. We compared bee diversity (richness, abundance and composition) in secondary forests of different age and coffee plantations with diverse farming techniques. Being the first study of pollinators in Guatemalan coffee plantations, we also recorded data for an entire year (2013–2014) in order to describe bee seasonality.
Results
We found significant differences in bee diversity between the coffee plantations and secondary forests, particularly early secondary forests showed higher bee abundances but diversity indices were similar between different vegetation type plots. In the early dry season, secondary forests showed the greatest native bee diversity. During the late dry season, when the coffee was flowering, honey bees were dominant in the same plots. This study provides important management insights to support the conservation of pollinators, since our results offer guidelines to improve coffee production by increasing native pollinator diversity.

Background

Although conservation of pristine habitats is recognized in many countries as crucial for maintaining pollinator diversity, the contribution of secondary forest conservation is poorly recognized in the Latin American context, such as in Guatemala. San Lucas Tolimán (SLT) is a high-quality coffee production region from the Atitlan Province, which has the second highest deciduous forest cover in Guatemala and pristine forest is prioritized for conservation. In contrast, secondary forest protection is undetermined, since these forests are normally removed or strongly affected by coffee farming practices. This situation may affect the diversity of native pollinators, mainly bees, which usually rely on the secondary forest for food resources.

Methods

We conducted a study to investigate the importance of secondary forests around the SLT coffee plantations (Coffea arabica L.) for pollinators. We compared bee diversity (richness, abundance and composition) in secondary forests of different age and coffee plantations with diverse farming techniques. Being the first study of pollinators in Guatemalan coffee plantations, we also recorded data for an entire year (2013–2014) in order to describe bee seasonality.

Results

We found significant differences in bee diversity between the coffee plantations and secondary forests, particularly early secondary forests showed higher bee abundances but diversity indices were similar between different vegetation type plots. In the early dry season, secondary forests showed the greatest native bee diversity. During the late dry season, when the coffee was flowering, honey bees were dominant in the same plots. This study provides important management insights to support the conservation of pollinators, since our results offer guidelines to improve coffee production by increasing native pollinator diversity.

Exogenous hormones influence Brassica napus leaf cuticular wax deposition and cuticle functionhttps://peerj.com/articles/92642020-06-042020-06-04Zheng YuanYouwei JiangYuhua LiuYi XuShuai LiYanjun GuoReinhard JetterYu Ni
Background
Cuticular waxes cover plant surface and play important roles in protecting plants from abiotic and biotic stresses. The variations of wax deposition and chemical compositions under changing environments have been shown to be related to plant adaptations. However, it is still not clear whether the wax depositions could be adjusted to increase plant adaptations to stressed conditions.
Methods
In this study, exogenous methyl jasmonate (MeJA), the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) and salicylic acid (SA) were applied to test their effects on cuticular wax deposition in two Brassica napus cultivars, Zhongshuang 9 (ZS9, low wax coverage ) and Yuyou 19 (YY19, high wax coverage). Next, we measured the water loss rate and the transcriptional expression of genes involved in wax biosynthesis as well as genes related to disease defense.
Results
Seven wax compound classes, including fatty acids, aldehydes, alkanes, secondary alcohols, ketones, and unbranched as well as branched primary alcohols, were identified in B. napus leaf wax mixtures. MeJA, SA and ACC treatments had no significant effect on total wax amounts in YY19, whereas ACC reduced total wax amounts in ZS9. Overall, hormone treatments led to an increase in the amounts of aldehydes and ketones, and a decrease of secondary alcohol in ZS9, whereas they led to a decrease of alkane amounts and an increase of secondary alcohol amounts in YY19. Concomitantly, both cultivars also exhibited different changes in cuticle permeability, with leaf water loss rate per 15 min increased from 1.57% (averaged across treatments) at 1.57% (averaged across treatments) at 15 min to 3.12% at 30 min for ZS9 (except for ACC treated plant) and decreased for YY19. MeJA-treated plants of both cultivars relatively had higher water loss rate per 15 min when compared to other treatments. Conclusion. Our findings that B. napus leaf wax composition and cuticle permeability are altered by exogenous SA, MeJA and ACC suggest that the hormone treatments affect wax composition, and that the changes in wax profiles would cause changes in cuticle permeability.

Background

Cuticular waxes cover plant surface and play important roles in protecting plants from abiotic and biotic stresses. The variations of wax deposition and chemical compositions under changing environments have been shown to be related to plant adaptations. However, it is still not clear whether the wax depositions could be adjusted to increase plant adaptations to stressed conditions.

Methods

In this study, exogenous methyl jasmonate (MeJA), the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) and salicylic acid (SA) were applied to test their effects on cuticular wax deposition in two Brassica napus cultivars, Zhongshuang 9 (ZS9, low wax coverage ) and Yuyou 19 (YY19, high wax coverage). Next, we measured the water loss rate and the transcriptional expression of genes involved in wax biosynthesis as well as genes related to disease defense.

Results

Seven wax compound classes, including fatty acids, aldehydes, alkanes, secondary alcohols, ketones, and unbranched as well as branched primary alcohols, were identified in B. napus leaf wax mixtures. MeJA, SA and ACC treatments had no significant effect on total wax amounts in YY19, whereas ACC reduced total wax amounts in ZS9. Overall, hormone treatments led to an increase in the amounts of aldehydes and ketones, and a decrease of secondary alcohol in ZS9, whereas they led to a decrease of alkane amounts and an increase of secondary alcohol amounts in YY19. Concomitantly, both cultivars also exhibited different changes in cuticle permeability, with leaf water loss rate per 15 min increased from 1.57% (averaged across treatments) at 1.57% (averaged across treatments) at 15 min to 3.12% at 30 min for ZS9 (except for ACC treated plant) and decreased for YY19. MeJA-treated plants of both cultivars relatively had higher water loss rate per 15 min when compared to other treatments. Conclusion. Our findings that B. napus leaf wax composition and cuticle permeability are altered by exogenous SA, MeJA and ACC suggest that the hormone treatments affect wax composition, and that the changes in wax profiles would cause changes in cuticle permeability.

Culicidae-centric metabarcoding through targeted use of D2 ribosomal DNA primershttps://peerj.com/articles/90572020-06-032020-06-03Pedro M. PedroJandui AmorimMartha V.R. RojasIvy Luizi SáAllan Kardec Ribeiro GalardoNoel Fernandes Santos NetoDario Pires de CarvalhoKaio Augusto Nabas RibeiroMaria Tereza Pepe RazzoliniMaria Anice Mureb Sallum
A practical limitation to many metabarcoding initiatives is that sampling methods tend to collect many non-target taxa, which become “amplicon noise” that can saturate Next Generation Sequencing results and lead to both financial and resource inefficiencies. An available molecular tool that can significantly decrease these non-target amplicons and decrease the need for pre-DNA-extraction sorting of bycatch is the design of PCR primers tailored to the taxa under investigation. We assessed whether the D2 extension segment of the 28S ribosomal operon can limit this shortcoming within the context of mosquito (Culicidae) monitoring. We designed PCR primers that are fully conserved across mosquitos and exclude from amplification most other taxa likely to be collected with current sampling apparatuses. We show that, given enough sequencing depth, D2 is an effective marker for the detection of mosquito sequences within mock genomic DNA pools. As few as 3,050 quality-filtered Illumina reads were able to recover all 17 species in a bulk pool containing as little as 0.2% of constituent DNA from single taxa. We also mixed these mosquito DNA pools with high concentrations of non-Culicidae bycatch DNA and show that the component mosquito species are generally still recoverable and faithful to their original relative frequencies. Finally, we show that there is little loss of fidelity in abundance parameters when pools from degraded DNA samples were sequenced using the D2 primers.

A practical limitation to many metabarcoding initiatives is that sampling methods tend to collect many non-target taxa, which become “amplicon noise” that can saturate Next Generation Sequencing results and lead to both financial and resource inefficiencies. An available molecular tool that can significantly decrease these non-target amplicons and decrease the need for pre-DNA-extraction sorting of bycatch is the design of PCR primers tailored to the taxa under investigation. We assessed whether the D2 extension segment of the 28S ribosomal operon can limit this shortcoming within the context of mosquito (Culicidae) monitoring. We designed PCR primers that are fully conserved across mosquitos and exclude from amplification most other taxa likely to be collected with current sampling apparatuses. We show that, given enough sequencing depth, D2 is an effective marker for the detection of mosquito sequences within mock genomic DNA pools. As few as 3,050 quality-filtered Illumina reads were able to recover all 17 species in a bulk pool containing as little as 0.2% of constituent DNA from single taxa. We also mixed these mosquito DNA pools with high concentrations of non-Culicidae bycatch DNA and show that the component mosquito species are generally still recoverable and faithful to their original relative frequencies. Finally, we show that there is little loss of fidelity in abundance parameters when pools from degraded DNA samples were sequenced using the D2 primers.

Simultaneous determination of phenolic metabolites in Chinese citrus and grape cultivarshttps://peerj.com/articles/90832020-06-032020-06-03Yuan ChenYanyun HongDaofu YangZhigang HeXiaozi LinGuojun WangWenquan Yu
Background
As the major bioactive compounds in citrus and grape, it is significant to use the contents of flavonoids and phenolic acids as quality evaluation criteria to provide a better view of classifying the quality and understanding the potential health benefits of each fruit variety.
Methods
A total of 15 varieties of citrus and 12 varieties of grapes were collected from Fujian, China. High-performance liquid chromatography method was used for the simultaneous determination of 17 phenolic compounds, including gallic acid, chlorogenic acid, caffeic acid, syringic acid, ρ-coumaric acid, ferulic acid, benzoic acid, salicylic acid, catechin, epicatechin, resveratrol, rutin, naringin, hesperidin, quercetin, nobiletin and tangeritin in the peels of citrus and grape cultivars. Further, the cultivars of citrus and grape were classified using principal component analysis (PCA) and hierarchical cluster analysis (HCA).
Results
A thorough separation of the 17 compounds was achieved within 100 min. The tested method exhibited good linearity (the limits of detection and limits of quantification were in the range of 0.03–1.83 µg/mL and 0.09–5.55 µg/mL, respectively), precision (the relative standard deviations of repeatability were 1.02–1.97%), and recovery (92.2–102.82%) for all the compounds, which could be used for the simultaneous determination of phenolic compounds in citrus and grape. Hesperidin (12.93–26,160.98 µg/g DW) and salicylic acid (5.35–751.02 µg/g DW) were the main flavonoids and phenolic acids in 15 citrus varieties, respectively. Besides, the hesperidin (ND to 605.48 µg/g DW) and salicylic acid (ND to 1,461.79 µg/g DW) were found as the highest flavonoid and the most abundant phenolic acid in grapes, respectively. A total of 15 citrus and 12 grape samples were classified into two main groups by PCA and HCA with strong consistency.

Background

As the major bioactive compounds in citrus and grape, it is significant to use the contents of flavonoids and phenolic acids as quality evaluation criteria to provide a better view of classifying the quality and understanding the potential health benefits of each fruit variety.

A thorough separation of the 17 compounds was achieved within 100 min. The tested method exhibited good linearity (the limits of detection and limits of quantification were in the range of 0.03–1.83 µg/mL and 0.09–5.55 µg/mL, respectively), precision (the relative standard deviations of repeatability were 1.02–1.97%), and recovery (92.2–102.82%) for all the compounds, which could be used for the simultaneous determination of phenolic compounds in citrus and grape. Hesperidin (12.93–26,160.98 µg/g DW) and salicylic acid (5.35–751.02 µg/g DW) were the main flavonoids and phenolic acids in 15 citrus varieties, respectively. Besides, the hesperidin (ND to 605.48 µg/g DW) and salicylic acid (ND to 1,461.79 µg/g DW) were found as the highest flavonoid and the most abundant phenolic acid in grapes, respectively. A total of 15 citrus and 12 grape samples were classified into two main groups by PCA and HCA with strong consistency.

Incorporating reef fish avoidance behavior improves accuracy of species distribution modelshttps://peerj.com/articles/92462020-06-032020-06-03Kostantinos A. StamoulisJade M.S. DelevauxIvor D. WilliamsAlan M. FriedlanderJake ReichardKeith KamikawaEuan S. Harvey
Species distribution models (SDMs) are used to interpret and map fish distributions based on habitat variables and other drivers. Reef fish avoidance behavior has been shown to vary in the presence of divers and is primarily driven by spearfishing pressure. Diver avoidance behavior or fish wariness may spatially influence counts and other descriptive measures of fish assemblages. Because fish assemblage metrics are response variables for SDMs, measures of fish wariness may be useful as predictors in SDMs of fishes targeted by spearfishing. We used a diver operated stereo-video system to conduct fish surveys and record minimum approach distance (MAD) of targeted reef fishes inside and outside of two marine reserves on the island of Oʻahu in the main Hawaiian Islands. By comparing MAD between sites and management types we tested the assumption that it provides a proxy for fish wariness related to spearfishing pressure. We then compared the accuracy of SDMs which included MAD as a predictor with SDMs that did not. Individual measures of MAD differed between sites though not management types. When included as a predictor, MAD averaged at the transect level greatly improved the accuracy of SDMs of targeted fish biomass.

Species distribution models (SDMs) are used to interpret and map fish distributions based on habitat variables and other drivers. Reef fish avoidance behavior has been shown to vary in the presence of divers and is primarily driven by spearfishing pressure. Diver avoidance behavior or fish wariness may spatially influence counts and other descriptive measures of fish assemblages. Because fish assemblage metrics are response variables for SDMs, measures of fish wariness may be useful as predictors in SDMs of fishes targeted by spearfishing. We used a diver operated stereo-video system to conduct fish surveys and record minimum approach distance (MAD) of targeted reef fishes inside and outside of two marine reserves on the island of Oʻahu in the main Hawaiian Islands. By comparing MAD between sites and management types we tested the assumption that it provides a proxy for fish wariness related to spearfishing pressure. We then compared the accuracy of SDMs which included MAD as a predictor with SDMs that did not. Individual measures of MAD differed between sites though not management types. When included as a predictor, MAD averaged at the transect level greatly improved the accuracy of SDMs of targeted fish biomass.

Addressing initialisation uncertainty for end-to-end ecosystem models: application to the Chatham Rise Atlantis modelhttps://peerj.com/articles/92542020-06-032020-06-03Vidette L. McGregorElizabeth A. FultonMatthew R. Dunn
Ecosystem models require the specification of initial conditions, and these initial conditions have some level of uncertainty. It is important to allow for uncertainty when presenting model results, because it reduces the risk of errant or non-representative results. It is crucial that model results are presented as an envelope of what is likely, rather than presenting only one instance. We perturbed the initial conditions of the Chatham Rise Atlantis model and analysed the effect of this uncertainty on the model’s dynamics by comparing the model outputs resulting from many initial condition perturbations. At the species group level, we found some species groups were more sensitive than others, with lower trophic level species groups generally more sensitive to perturbations of the initial conditions. We recommend testing for robust system dynamics by assessing the consistency of ecosystem indicators in response to fishing pressure under perturbed initial conditions. In any set of scenarios explored using complex end-to-end ecosystem models, we recommend that associated uncertainty analysis be included with perturbations of the initial conditions.

Ecosystem models require the specification of initial conditions, and these initial conditions have some level of uncertainty. It is important to allow for uncertainty when presenting model results, because it reduces the risk of errant or non-representative results. It is crucial that model results are presented as an envelope of what is likely, rather than presenting only one instance. We perturbed the initial conditions of the Chatham Rise Atlantis model and analysed the effect of this uncertainty on the model’s dynamics by comparing the model outputs resulting from many initial condition perturbations. At the species group level, we found some species groups were more sensitive than others, with lower trophic level species groups generally more sensitive to perturbations of the initial conditions. We recommend testing for robust system dynamics by assessing the consistency of ecosystem indicators in response to fishing pressure under perturbed initial conditions. In any set of scenarios explored using complex end-to-end ecosystem models, we recommend that associated uncertainty analysis be included with perturbations of the initial conditions.